Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex

Tiffany Ge; Donna Garvey Brickner; Kara Zehr; D. Jake VanBelzen; Wenzhu Zhang; Christopher Caffalette; Gavin C. Moeller; Sara Ungerleider; Nikita Marcou; Alexis Jacob; Vu Q. Nguyen; Brian Chait; Michael P. Rout; Jason H. Brickner

doi:10.1016/j.molcel.2025.02.013

Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex

Tiffany Ge, Donna Garvey Brickner, Kara Zehr, D. Jake VanBelzen, Wenzhu Zhang, Christopher Caffalette, Gavin C. Moeller, Sara Ungerleider, Nikita Marcou, Alexis Jacob, Vu Q. Nguyen, Brian Chait, Michael P. Rout, Jason H. Brickner^*

^*Corresponding author for this work

Molecular Biosciences

Research output: Contribution to journal › Article › peer-review

Abstract

Nuclear pore proteins (nucleoporins [Nups]) physically interact with hundreds of chromosomal sites, impacting transcription. In yeast, transcription factors mediate interactions between Nups and enhancers and promoters. To define the molecular basis of this mechanism, we exploited a separation-of-function mutation in the Gcn4 transcription factor that blocks its interaction with the nuclear pore complex (NPC). This mutation reduces the interaction of Gcn4 with the highly conserved nuclear export factor Crm1/Xpo1. Crm1 and Nups co-occupy enhancers, and Crm1 inhibition blocks interaction of the nuclear pore protein Nup2 with the genome. In vivo, Crm1 interacts stably with the NPC and in vitro, Crm1 binds directly to both Gcn4 and Nup2. Importantly, the interaction between Crm1 and Gcn4 requires neither Ran-guanosine triphosphate (GTP) nor the nuclear export sequence binding site. Finally, Crm1 and Ran-GTP stimulate DNA binding by Gcn4, suggesting that allosteric coupling between Crm1-Ran-GTP binding and DNA binding facilitates the docking of transcription-factor-bound enhancers at the NPC.

Original language	English (US)
Pages (from-to)	1101-1116.e8
Journal	Molecular cell
Volume	85
Issue number	6
DOIs	https://doi.org/10.1016/j.molcel.2025.02.013
State	Published - Mar 20 2025

Funding

The authors thank Professor Eric Weiss (Northwestern) for sharing the crm1-T539C strains, Professor Reza Vafabakhsh (Northwestern) for sharing nanobody-coupled beads, Winny Liu for help with plasmid construction, Dr. Atsushi Satomura for help developing SLAM-seq and ChEC-seq2, Dr. Trevor Van Eeuwen (Rockefeller) for help with figures, and members of the Brickner laboratory for helpful comments on the manuscript. This work was supported by NIH grants R35GM136419 (J.H.B.), P41 GM109824 (M.P.R. and B.C.), R01 GM112108 (M.P.R.), T32 NIGMS GM008061 (T.G. and D.J.V.), and F32 GM153164 (C.C.) and a predoctoral fellowship from the National Science Foundation (D.J.V.). The authors thank Professor Eric Weiss (Northwestern) for sharing the crm1-T539C strains, Professor Reza Vafabakhsh (Northwestern) for sharing nanobody-coupled beads, Winny Liu for help with plasmid construction, Dr. Trevor Van Eeuwen (Rockefeller) for help with figures, and members of the Brickner laboratory for helpful comments on the manuscript. This work was supported by NIH grants R35GM136419 (J.H.B.), P41 GM109824 (M.P.R. and B.C.), R01 GM112108 (M.P.R.), T32 NIGMS GM008061 (T.G. and D.J.V.), and F32 GM153164 (C.C.) and a predoctoral fellowship from the National Science Foundation (D.J.V.).

Keywords

nuclear architecture
nuclear pore complex
transcription
transcription factor

ASJC Scopus subject areas

Molecular Biology
Cell Biology

Access to Document

10.1016/j.molcel.2025.02.013

Cite this

Ge, T., Brickner, D. G., Zehr, K., VanBelzen, D. J., Zhang, W., Caffalette, C., Moeller, G. C., Ungerleider, S., Marcou, N., Jacob, A., Nguyen, V. Q., Chait, B., Rout, M. P., & Brickner, J. H. (2025). Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex. Molecular cell, 85(6), 1101-1116.e8. https://doi.org/10.1016/j.molcel.2025.02.013

@article{b2229c0b1fc549a08483a6a1a6070448,

title = "Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex",

abstract = "Nuclear pore proteins (nucleoporins [Nups]) physically interact with hundreds of chromosomal sites, impacting transcription. In yeast, transcription factors mediate interactions between Nups and enhancers and promoters. To define the molecular basis of this mechanism, we exploited a separation-of-function mutation in the Gcn4 transcription factor that blocks its interaction with the nuclear pore complex (NPC). This mutation reduces the interaction of Gcn4 with the highly conserved nuclear export factor Crm1/Xpo1. Crm1 and Nups co-occupy enhancers, and Crm1 inhibition blocks interaction of the nuclear pore protein Nup2 with the genome. In vivo, Crm1 interacts stably with the NPC and in vitro, Crm1 binds directly to both Gcn4 and Nup2. Importantly, the interaction between Crm1 and Gcn4 requires neither Ran-guanosine triphosphate (GTP) nor the nuclear export sequence binding site. Finally, Crm1 and Ran-GTP stimulate DNA binding by Gcn4, suggesting that allosteric coupling between Crm1-Ran-GTP binding and DNA binding facilitates the docking of transcription-factor-bound enhancers at the NPC.",

keywords = "nuclear architecture, nuclear pore complex, transcription, transcription factor",

author = "Tiffany Ge and Brickner, {Donna Garvey} and Kara Zehr and VanBelzen, {D. Jake} and Wenzhu Zhang and Christopher Caffalette and Moeller, {Gavin C.} and Sara Ungerleider and Nikita Marcou and Alexis Jacob and Nguyen, {Vu Q.} and Brian Chait and Rout, {Michael P.} and Brickner, {Jason H.}",

note = "Publisher Copyright: {\textcopyright} 2025 Elsevier Inc.",

year = "2025",

month = mar,

day = "20",

doi = "10.1016/j.molcel.2025.02.013",

language = "English (US)",

volume = "85",

pages = "1101--1116.e8",

journal = "Molecular cell",

issn = "1097-2765",

publisher = "Cell Press",

number = "6",

}

Ge, T, Brickner, DG, Zehr, K, VanBelzen, DJ, Zhang, W, Caffalette, C, Moeller, GC, Ungerleider, S, Marcou, N, Jacob, A, Nguyen, VQ, Chait, B, Rout, MP & Brickner, JH 2025, 'Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex', Molecular cell, vol. 85, no. 6, pp. 1101-1116.e8. https://doi.org/10.1016/j.molcel.2025.02.013

TY - JOUR

T1 - Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex

AU - Ge, Tiffany

AU - Brickner, Donna Garvey

AU - Zehr, Kara

AU - VanBelzen, D. Jake

AU - Zhang, Wenzhu

AU - Caffalette, Christopher

AU - Moeller, Gavin C.

AU - Ungerleider, Sara

AU - Marcou, Nikita

AU - Jacob, Alexis

AU - Nguyen, Vu Q.

AU - Chait, Brian

AU - Rout, Michael P.

AU - Brickner, Jason H.

PY - 2025/3/20

Y1 - 2025/3/20

N2 - Nuclear pore proteins (nucleoporins [Nups]) physically interact with hundreds of chromosomal sites, impacting transcription. In yeast, transcription factors mediate interactions between Nups and enhancers and promoters. To define the molecular basis of this mechanism, we exploited a separation-of-function mutation in the Gcn4 transcription factor that blocks its interaction with the nuclear pore complex (NPC). This mutation reduces the interaction of Gcn4 with the highly conserved nuclear export factor Crm1/Xpo1. Crm1 and Nups co-occupy enhancers, and Crm1 inhibition blocks interaction of the nuclear pore protein Nup2 with the genome. In vivo, Crm1 interacts stably with the NPC and in vitro, Crm1 binds directly to both Gcn4 and Nup2. Importantly, the interaction between Crm1 and Gcn4 requires neither Ran-guanosine triphosphate (GTP) nor the nuclear export sequence binding site. Finally, Crm1 and Ran-GTP stimulate DNA binding by Gcn4, suggesting that allosteric coupling between Crm1-Ran-GTP binding and DNA binding facilitates the docking of transcription-factor-bound enhancers at the NPC.

AB - Nuclear pore proteins (nucleoporins [Nups]) physically interact with hundreds of chromosomal sites, impacting transcription. In yeast, transcription factors mediate interactions between Nups and enhancers and promoters. To define the molecular basis of this mechanism, we exploited a separation-of-function mutation in the Gcn4 transcription factor that blocks its interaction with the nuclear pore complex (NPC). This mutation reduces the interaction of Gcn4 with the highly conserved nuclear export factor Crm1/Xpo1. Crm1 and Nups co-occupy enhancers, and Crm1 inhibition blocks interaction of the nuclear pore protein Nup2 with the genome. In vivo, Crm1 interacts stably with the NPC and in vitro, Crm1 binds directly to both Gcn4 and Nup2. Importantly, the interaction between Crm1 and Gcn4 requires neither Ran-guanosine triphosphate (GTP) nor the nuclear export sequence binding site. Finally, Crm1 and Ran-GTP stimulate DNA binding by Gcn4, suggesting that allosteric coupling between Crm1-Ran-GTP binding and DNA binding facilitates the docking of transcription-factor-bound enhancers at the NPC.

KW - nuclear architecture

KW - nuclear pore complex

KW - transcription

KW - transcription factor

UR - http://www.scopus.com/inward/record.url?scp=86000728523&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=86000728523&partnerID=8YFLogxK

U2 - 10.1016/j.molcel.2025.02.013

DO - 10.1016/j.molcel.2025.02.013

M3 - Article

C2 - 40068679

AN - SCOPUS:86000728523

SN - 1097-2765

VL - 85

SP - 1101-1116.e8

JO - Molecular cell

JF - Molecular cell

IS - 6

ER -

Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex

Abstract

Funding

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this